Plotting individual home range centers

[f.christiansen]

I was wondering if there is some other way than the fxi.contour function to plot individual home range centers for marked individuals? fxi.contour would be the obvious choice, but unfortunately I have some sampling occasions during which some detectors are not used (a pre-requisite for using fxi.contour). Any help would be greatly appreciated.

[murray.efford]

I was wondering if there is some other way than the fxi.contour function to plot individual home range centers for marked individuals? fxi.contour would be the obvious choice, but unfortunately I have some sampling occasions during which some detectors are not used (a pre-requisite for using fxi.contour).

I blocked incomplete layouts with fxi.contour merely because I hadn't tested them. It seems they work fine (example below), although computation is very slow, as with fitting such models, and the effect will usually be trivial. I have enabled incomplete layouts in my working copy of 2.4.1: contact me offline and I can send you a link.
Murray

Code: Select all

library(secr)  ## requires >= 2.4.1

## add phony 'usage' attribute to test dataset
usage(traps(captdata)) <- matrix(1, nrow = 100, ncol = 5)
usage(traps(captdata))[c(13,17:19),] <- 0

## try fitting with phony usage
fitCL <- secr.fit(captdata, CL = TRUE)

## plot to compare
par(mfrow = c(1,2))
plot(traps(captdata), markused = TRUE, main = 'ID 5')
fxi.contour(secrdemo.CL, i = 5, plotmode = TRUE, add = TRUE)
plot(traps(captdata), markused = TRUE, main = 'ID 5; Allowing for traps 13, 17:19 not used')
fxi.contour(fitCL, i = 5, plotmode = TRUE, add = TRUE, col='blue')


[murray.efford]

...although computation is very slow, as with fitting such models...

For the record: execution given variable 'usage' was slow only with exclusive detectors (e.g., multi-catch traps 'multi', exclusive polygons 'polygonX'), and could be sped up even for these cases. See next release.

[f.christiansen]

It works now, thank you very much. Its a bit slow to plot individual home range centers, but I think on a better (faster) computer it would not be a problem. Thank you very much!